I am using the following function (and is looped through the pairs of
unique sets of gradient tables (i.e. loops twice for dir99 and dir98):
${HCPPIPEDIR}/DiffusionPreprocessing/DiffPreprocPipeline.sh \
--posData="{posData}" \
--negData="{negData}" \
--path="{path}" \
--subject="{subject}" \
--echospacing="{echospacing}" \
--PEdir={PEdir} \
--gdcoeffs="NONE" \
--dwiname="{dwiname}" \
--printcom=""'
Where:
$posData = diffusion data in the positive direction
$negData = diffusion data in the negative direction
$path = output directory path
$echospacing = echospacing
$PEdir = 2
$dwiname = i.e. Diffusion_dir-98_run-01
FYI: I'm using HCPPipelines v3.17.
-------------------------------------------------------------
Technical details:
I run ${HCPPIPEDIR}/DiffusionPreprocessing/DiffPreprocPipeline.sh in a
Docker container with the following python code. It is looped through the
pairs of unique sets of gradient tables (i.e. loops twice for dir99 and
dir98) and set to process in parallel:
dwi_stage_dict = OrderedDict([("DiffusionPreprocessing",
partial(run_diffusion_processsing,
*posData*=pos,
*negData*=neg,
*path*=args.output_dir,
*subject*="sub-%s" % subject_label,
*echospacing*=echospacing,
*PEdir*=PEdir,
*gdcoeffs*="NONE",
*dwiname*=dwiname,
*n_cpus*=args.n_cpus))])
for stage, stage_func in
dwi_stage_dict.iteritems():
if stage in args.stages:
Process(target=stage_func).start()
On Mon, Jul 17, 2017 at 11:15 AM, Glasser, Matthew <glass...@wustl.edu>
wrote:
> The pipeline is capable of doing the merge for you if you want. Can you
> post how you called the diffusion pipeline?
>
> Peace,
>
> Matt.
>
> From: Yeun Kim <yeun...@gmail.com>
> Date: Monday, July 17, 2017 at 1:12 PM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] diffusion data merge pipeline
>
> When I run DiffusionPreprocessing, I make the --dwiname=DWIName specific
> to the diffusion scan (i.e. DWIName= Diffusion_dir-98_run-01) to prevent
> files from being overwritten.
> I end up with:
> ${StudyFolder}/${Subject}/T1w/Diffusion_dir-98_run-01/data.nii.gz
> ${StudyFolder}/${Subject}/T1w/Diffusion_dir-99_run-01/data.nii.gz
>
> I would like to combine the two data.nii.gz files.
>
> On Mon, Jul 17, 2017 at 10:58 AM, Glasser, Matthew <glass...@wustl.edu>
> wrote:
>
>> Look for the ${StudyFolder}/${Subject}/T1w/Diffusion/data.nii.gz file.
>>
>> Peace,
>>
>> Matt.
>>
>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Yeun Kim <
>> yeun...@gmail.com>
>> Date: Monday, July 17, 2017 at 12:56 PM
>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: [HCP-Users] diffusion data merge pipeline
>>
>> Hi,
>>
>> We have the diffusion scans:
>> dMRI_dir98_AP, dMRI_dir98_PA
>> dMRI_dir99_AP, dMRI_dir99_PA
>>
>> in which there is a pair of phase encoding directions (AP,PA) and two
>> sets of different diffusion weighting directions (dir98 and dir99).
>>
>> After running the DiffusionPreprocessing module of the HCP minimal
>> preprocessing pipeline, I would like to merge the processed dMRI_dir98 and
>> dMRI_dir99 data. Do you have any suggestions on how to perform this step?
>> Also, are there any workflows developed by HCP for
>> post-DiffusionPreprocessing?
>>
>> Thank you,
>> Yeun
>>
>> _______________________________________________
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>
>
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